<h1 class="title" id="page-title">Taxoner Server: Introduction</h1>

<b>Taxoner</b>, a simple, paralellizeable workflow that uses database partitioning in 
conjunction with <a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml">Bowtie2</a>
searches, which allows one to align millions of reads against the full
<a href="ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz">nt</a> database of 
<a href="https://www.ncbi.nlm.nih.gov">NCBI</a>, typically in a few hours on a standard 
four threaded processor.

The program can accept reads of all major platforms (Illumina, Ion Torrent, 454,
PacBio) and the output can be either further analyzed with sophisticated tools
such as <a href="http://ab.inf.uni-tuebingen.de/software/megan/">MEGAN</a>, or directly
evaluated by a built-in taxon assignment procedure that also allows the 
identification of genes and potential functions.

The speed and accuracy of the method compares favorably to other programs and 
it can run on ordinary desktop or laptop computers without significant loss in speed.
